| Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions L Narunsky-Haziza, GD Sepich-Poore, I Livyatan, O Asraf, C Martino, ... Cell 185 (20), 3789-3806. e17, 2022 | 317 | 2022 |
| Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity RC Kaplan, Z Wang, M Usyk, D Sotres-Alvarez, ML Daviglus, ... Genome biology 20, 1-21, 2019 | 144 | 2019 |
| Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome BC Taylor, F Lejzerowicz, M Poirel, JP Shaffer, L Jiang, A Aksenov, ... Msystems 5 (2), 10.1128/msystems. 00901-19, 2020 | 140 | 2020 |
| Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range … Z Chen, L Pham, TC Wu, G Mo, Y Xia, PL Chang, D Porter, T Phan, H Che, ... Genome research 30 (6), 898-909, 2020 | 104 | 2020 |
| Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity JP Shaffer, LF Nothias, LR Thompson, JG Sanders, RA Salido, ... Nature Microbiology 7 (12), 2128-2150, 2022 | 103 | 2022 |
| An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae) JP Shaffer, JM U'Ren, RE Gallery, DA Baltrus, AE Arnold Frontiers in microbiology 8, 350, 2017 | 85 | 2017 |
| Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy Q Zhu, S Huang, A Gonzalez, I McGrath, D McDonald, N Haiminen, ... Msystems 7 (2), e00167-22, 2022 | 53 | 2022 |
| Bacterial endosymbionts: master modulators of fungal phenotypes SJ Araldi-Brondolo, J Spraker, JP Shaffer, EH Woytenko, DA Baltrus, ... Microbiology spectrum 5 (5), 10.1128/microbiolspec. funk-0056-2016, 2017 | 53 | 2017 |
| Enhancing untargeted metabolomics using metadata-based source annotation JM Gauglitz, KA West, W Bittremieux, CL Williams, KC Weldon, ... Nature biotechnology 40 (12), 1774-1779, 2022 | 50 | 2022 |
| Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves JP Shaffer, C Sarmiento, PC Zalamea, RE Gallery, AS Davis, DA Baltrus, ... Frontiers in Ecology and Evolution 4, 116, 2016 | 50 | 2016 |
| SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment C Marotz, P Belda-Ferre, F Ali, P Das, S Huang, K Cantrell, L Jiang, ... Microbiome 9 (1), 132, 2021 | 48 | 2021 |
| Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California TL Alderete, RB Jones, JP Shaffer, EA Holzhausen, WB Patterson, ... Gut microbes 13 (1), 1961203, 2021 | 48 | 2021 |
| Microbiome metadata standards: report of the National Microbiome Data Collaborative’s workshop and follow-on activities P Vangay, J Burgin, A Johnston, KL Beck, DC Berrios, K Blumberg, ... Msystems 6 (1), 10.1128/msystems. 01194-20, 2021 | 46 | 2021 |
| A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities JP Shaffer, CS Carpenter, C Martino, RA Salido, JJ Minich, MK Bryant, ... Biotechniques 73 (1), 34-46, 2022 | 45 | 2022 |
| Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies M Usyk, BA Peters, S Karthikeyan, D McDonald, CC Sollecito, ... Cell reports methods 3 (1), 2023 | 41 | 2023 |
| A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities JP Shaffer, C Marotz, P Belda-Ferre, C Martino, S Wandro, M Estaki, ... Biotechniques 70 (3), 149-159, 2021 | 31 | 2021 |
| Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age MJ Bailey, EA Holzhausen, ZEM Morgan, N Naik, JP Shaffer, D Liang, ... Gut Microbes 14 (1), 2105096, 2022 | 26 | 2022 |
| Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants YM Li, JP Shaffer, B Hall, H Ko PLoS One 14 (10), e0224417, 2019 | 25 | 2019 |
| Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment JJ Minich, F Ali, C Marotz, P Belda-Ferre, L Chiang, JP Shaffer, ... Microbiome 9, 1-13, 2021 | 24 | 2021 |
| Context-dependent and variable effects of endohyphal bacteria on interactions between fungi and seeds JP Shaffer, PC Zalamea, C Sarmiento, RE Gallery, JW Dalling, AS Davis, ... Fungal Ecology 36, 117-127, 2018 | 22 | 2018 |